Phil Hugenholtz

New insights into the evolution and metabolism of the bacterial phylum Candidatus Acidulodesulfobacteriota through metagenomics - Environmental Microbiome Candidatus Acidulodesulfobacterales, a formerly proposed bacterial order within the Deltaproteobacteria lineage, represents an ecologically significant group in sulfur-rich environments. Their diversity and functional potential in artificial acid mine drainage (AMD) ecosystems have been well studied; however, their distribution and ecological role in marine hydrothermal sulfides remain poorly understood. Here we integrated publicly available metagenome-assembled genomes (MAGs) with a newly reconstructed MAG from hydrothermal sulfides to perform comprehensive phylogenetic, metabolic, and host-virus interaction analyses. Phylogenomic and 16S rRNA gene analyses indicated that this lineage represents a distinct phylum-level clade, leading us to propose the designation Ca. Acidulodesulfobacteriota. Metabolic reconstructions indicated a versatile lifestyle, encompassing pathways for carbon fixation, nitrogen fixation, sulfur metabolism, iron oxidation, and hydrogen oxidation. Notably, the concatenated DsrAB protein phylogeny and the mixed enzyme types involved in Dsr-dependent dissimilatory sulfur metabolism suggest that Ca. Acidulodesulfobacteriota may represent a transitional lineage in the evolutionary shift from reductive to oxidative Dsr metabolism. Viral auxiliary metabolic genes (AMGs) associated with this phylum were predicted to modulate host metabolic pathways, including folate biosynthesis and sulfur metabolism, highlighting intricate host-virus interactions. These findings advance our understanding of the evolution, metabolic potential, and ecological roles of Ca. Acidulodesulfobacteriota in biogeochemical cycling.

New insights into the evolution and metabolism of the bacterial phylum Candidatus Acidulodesulfobacteriota through metagenomics
#microbiology #bacteria
@microbiomej.bsky.social
environmentalmicrobiome.biomedcentral.com/articles/10....

Yeah, there is some silly stuff out there, e.g. “In the 7 years since first release, we have seen what appears to be some 226 revisions given the release of [GTDB] 10-RS226, dated April 16, 2025.”

Planetary microbiology: microbes, planets, and the search for life | Applied and Environmental Microbiology Life on Earth has existed for nearly 4 billion years, and for most of that time, it was microbial (1). The diverse world we see around us today owes its entire existence to a few foundational events c...

Planetary microbiology explores how ancient microbial innovations reshaped our planet and continue to guide our search for life on Mars, Europa, and across the cosmos.

New editorial from the lab: journals.asm.org/doi/10.1128/... @asm.org

The genomic basis of symbiotic integration at University of Bath on FindAPhD.com PhD Project - The genomic basis of symbiotic integration at University of Bath, listed on FindAPhD.com

There's a PhD position now available with me in Bath, on the evolution of symbiosis. www.findaphd.com/phds/project.... The supervisory team also includes @anja1.bsky.social @phil-donoghue.bsky.social and others. NB, this is open both to UK-based students *and* to international students :)

‘Google for DNA’ brings order to biology’s big data MetaGraph compresses vast data archives into a search engine for scientists, opening up new frontiers of biological discovery.

The Internet has Google. Now biology has MetaGraph. Detailed today in Nature, the search engine can quickly sift through the staggering volumes of biological data housed in public repositories. www.nature.com/articles/d41... #science #biology #biotech

Two full-time positions | Bioinformatician (m/f/d) + Applications Specialist (m/f/d) - Molecular Biology The Genome Facility at the Max Planck Institute for Evolutionary Biology in Plön is seeking to fill two positions (full time) to support and expand our core facility services.

Two new positions are available at the MPI for Evolutionary Biology to support development of our genomics facility. Both stand to become permanent. Both offer a ton of opportunity to engage in a wide range of creative science.

Pls repost 🙏

www.evolbio.mpg.de/3838377/job_...

A timetree of Fungi dated with fossils and horizontal gene transfers - Nature Ecology & Evolution Combining fossil-based and molecular calibrations with data on horizontal gene transfer events, the authors develop a time-calibrated phylogeny of Fungi. This timescale, which integrates analytic uncertainties, suggests an older age of crown Fungi (1,401–896 million years ago), as well as a minimum age for ancient interactions involving fungi and the algal ancestors of embryophytes in terrestrial ecosystems (1,253–797 Ma).

A paper in Nature Ecology & Evolution presents a time-calibrated phylogeny of Fungi. This timescale suggests an older age of crown Fungi, as well as a minimum age for ancient interactions involving fungi and the algal ancestors of embryophytes in terrestrial ecosystems. #phylo 🧪

A genomic view of the bacterial family Endozoicomonadaceae in marine symbioses - Communications Biology This review explores the genomic diversity, ecology, and functional potential of the bacterial family Endozoicomonadaceae in marine symbioses, highlighting their mutualistic to parasitic spectrum and key gaps to be addressed in future research.

A genomic view of the bacterial family Endozoicomonadaceae in marine symbioses
www.nature.com/articles/s42... #jcampubs

Genome-resolved insights into the bacterial phylum WOR-3: hydrogenotrophic metabolism and unique carbon fixation via archaeal form III RuBisCO | mSystems The WOR-3 phylum represents a widespread but poorly understood bacterial lineage inhabiting diverse various environments. By integrating 181 metagenome-assembled genomes, including 59 newly reconstruc...

Genome-resolved insights into the bacterial phylum WOR-3: hydrogenotrophic metabolism and unique carbon fixation via archaeal form III RuBisCO
journals.asm.org/doi/10.1128/... #jcampubs

Don't miss out on the 3rd West Pacific Marine Biology Symposium @ UQ Brisbane, 25–28 Nov.

Reg & abstracts open: tinyurl.com/wpmbs2025
Early-bird regos now extended to 14 Oct, so you can still secure discounted registration rates!

@cnrs.fr
@cnrsbiologie.bsky.social
UQ Centre for Marine Science

High-accuracy SNV calling for bacterial isolates using deep learning with AccuSNV Accurate detection of mutations within bacterial species is critical for fundamental studies of microbial evolution, reconstructing transmission events, and identifying antimicrobial resistance mutati...

Precisely calling mutations across hundreds of bacterial isolates has been hard, requiring manual filtering and expertise.

Until now, using AccuSNV.

Herui Liao trained an ML model based on our previous meticulously called SNVs.
www.biorxiv.org/content/10.1...

The role of mobile genetic elements in adaptation of the microbiota to the dynamic human gut ecosystem

#CurrOpinMicrobiol from @lgbacteria.bsky.social

www.sciencedirect.com/science/arti...

Uncover the hidden world of Fusobacterium watanabei! These eight clinical isolates reveal a genome size of 1.95-2.09 Mbp, shedding light on a lesser-known member of the Fusobacterium fami...

🧵 Thread below

Full analysis: https://helixbrief.com/article/693a54ad-af30-4449-a01b-4ad9576e5ca5

Little sneak-peek of per-site #eDNA reports we've been putting together - launching hopefully next week...

A global view of morphogenetic peptidoglycan synthases across the domain Bacteria Abstract. Bacteria define their heritable cell shape using membrane integral glycosyltransferases (GTases) of the shape, elongation, division and sporulati

A global view of morphogenetic peptidoglycan synthases across the domain Bacteria Open Access

@femsjournals.bsky.social microLife by Francisco García-del Portillo et al

academic.oup.com/microlife/ad...

Polysaccharide-degrading archaea dominate acidic hot springs: genomic and cultivation insights into a novel Thermoproteota lineage
Candidatus Marsarchaeota is now isolated and renamed as Tardisphaerales (phylum Thermoproteota) 🤓
@asm.org
journals.asm.org/doi/10.1128/...

Fantastic paper: "Dual transposon sequencing profiles the genetic interaction landscape in bacteria" out now in Science www.science.org/doi/10.1126/...

Thrilled to have contributed as part of the Data Reuse Consortium behind this new @natmicrobiol.nature.com article 'A roadmap for equitable reuse of public microbiome data'

www.nature.com/articles/s41...

If you work with microbiome, metagenomic, or ‘omics data more broadly, check out the paper.

I see 2030 in there 🙃

BONCAT-Live for isolation and cultivation of active environmental bacteria journals.asm.org/doi/full/10.... #jcampubs

A genomic view of Earth’s biomes - Nature Reviews Genetics Genome-wide approaches have uncovered the vast microbial and viral diversity across ecosystems. This Review explores advances in metagenomics, single-cell sequencing and functional profiling to elucid...

Sequencing methods 🧬 have come a long way from census counts 🔢 to assembling genomes and understanding the functions 🧪 of bacteria and viruses.

New review by @jgi.doe.gov's Gitta Szabó, @emileyeloe-fadrosh.bsky.social, Tanja Woyke with @jeffinerca.bsky.social

www.nature.com/articles/s41...

Phages with a broad host range are common across ecosystems - Nature Microbiology Proximity-ligation-based sequencing from 111 samples and 5 environments reveals that a substantial proportion of phages infect multiple species.

#NewResearch

Proximity-ligation-based sequencing from 111 samples and 5 environments reveals that a substantial proportion of phages infect multiple species

#MicroSky
@mmarbout.bsky.social @rkoszul.bsky.social @institutpasteur.bsky.social @cnrsbiologie.bsky.social

www.nature.com/articles/s41...

A dominant subgroup of marine Bathyarchaeia assimilates organic and inorganic carbon into unconventional membrane lipids - Nature Microbiology Baizosediminiarchaeum, a key player in the deep biosphere, builds butanetriol dialkyl glycerol tetraether (BDGT) membrane lipids and feeds on both CO2 and lignin, revealing a survival strategy in low-...

#NewResearch

Baizosediminiarchaeum, a key player in the deep biosphere, builds butanetriol dialkyl glycerol tetraether membrane lipids and feeds on both CO2 and lignin, revealing a survival strategy in low-energy environments.

#MicroSky

www.nature.com/articles/s41...

GenomeOcean Leverages AI to Decode Nature’s Secret Language | Joint Genome Institute Trained on environmental data, a new JGI tool more accurately facilitates microbial genome discoveries.

Trained on 600 Gbp of genetic data, most of which are available via JGI platforms, #GenomeOcean is an AI tool available to the global research community that facilitates microbial genome discoveries. Learn more below 🖥️ 🧬 🦠

@nersc.bsky.social @berkeleylab.lbl.gov @axelvisel.bsky.social

Structure of a functional archaellum in Bacteria of the Chloroflexota phylum - Nature Microbiology Bona fide gene clusters for archaella are widespread across a bacterial phylum and encode functional motility machinery.

#NewResearch

Structure of a functional archaellum in bacteria of the Chloroflexota phylum

#MicroSky

@archaellum.bsky.social @sshamphavi.bsky.social @loumollat.bsky.social ‬ @mariejoest.bsky.social @sgribaldo.bsky.social

www.nature.com/articles/s41...

Autocycler: long-read consensus assembly for bacterial genomes. #LongRead #SequneceData #GenomeAssembly #ConsensusAssembly #BacterialGenomes #Bioinformatics 🧬 🖥️
academic.oup.com/bioinformati...

Functional division of labor in motility, lignocellulose digestion, and nitrogen metabolism revealed for the Mixotricha paradoxa holobiont
#microbiology #protists #termites
@isme-microbes.bsky.social
academic.oup.com/ismej/articl...

Happy to see that Spacedust is now published on Nature Methods!
It combines sensitive Foldseek structure search and conserved neighborhood detection to discover functionally-associated gene clusters in prokaryotic & viral genomes.
1/6🧵

hey bluesky 👋 visa hurdles mean I’m looking for opportunities outside the US. I’m a computational biologist (bacterial + phage genomics, postdoc in Koonin’s group @ NIH). I am interested in teaming up on funding apps. reach out if this resonates!

Trace gas oxidation as a novel microbial dispersal trait
#microbiology #hydrogen #methane
www.sciencedirect.com/science/arti...